It's fairly easy to keep two iTunes libraries, one with only lossless files and the other with mp3's. If you hold down the 'Option' key when you launch iTunes on the Mac, or the 'Shift' key in Windows, you will be asked to select which library you want to use or whether you want to create a new one. Once it launches you plug in the iPod you want to use with those files and sync. I keep the lossless library on my computer and the mp3 library on a small external drive but you could do it the other way around or even have them both on the same drive.
There may be easier ways to do this but when I rip a CD to Apple Lossless I then select all those files in the library window and choose the menu item 'Create MP3 version'. Then I quit iTunes, hold down the option key and launch the other library, then drag the mp3 files from the iTunes music folder (not the library window) into iTunes. It sounds more complicated that it is.
If you have a lot of lossless and mp3 files mixed together in your original library you can use Spotlight (on the Mac) to search by file type for all the .mp3 files, move them to another place for import into the mp3 library and use iTunes itself to delete the entries for them in the library by sorting your songs by 'Kind.'
